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gabrielmoreira

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• 21k skills
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• 17 repo stars
• 2 weeks ago last updated

1. ▌
   Bio Workflows Outbreak Pipeline · gabrielmoreira bundle

   End-to-end outbreak investigation from pathogen isolates to transmission networks. Orchestrates MLST typing, AMR surveillance, phylodynamic dating, and transmission inference with TransPhylo. Use when investigating disease outbreaks or tracking pathogen transmission chains.
   17 repo stars
2. ▌
   Bio Pileup Generation · gabrielmoreira bundle

   Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.
   17 repo stars
3. ▌
   Bio Pathway Reactome · gabrielmoreira bundle

   Reactome pathway enrichment using ReactomePA package. Use when analyzing gene lists against Reactome's curated peer-reviewed pathway database. Performs over-representation analysis and GSEA with visualization and pathway hierarchy exploration.
   17 repo stars
4. ▌
   Bio Restriction Sites · gabrielmoreira bundle

   Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Search with single enzymes, batches of enzymes, or commercially available enzyme sets. Returns cut positions for linear or circular DNA. Use when finding restriction enzyme cut sites in sequences.
   17 repo stars
5. ▌
   Bio Scaffold Analysis · gabrielmoreira bundle

   Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.
   17 repo stars
6. ▌
   Bio Workflows Scrnaseq Pipeline · gabrielmoreira bundle

   End-to-end single-cell RNA-seq workflow from 10X Genomics data to annotated cell types. Covers QC, normalization, clustering, marker detection, and cell type annotation. Use when analyzing single-cell RNA-seq data.
   17 repo stars
7. ▌
   Bio Splicing Pipeline · gabrielmoreira bundle

   End-to-end alternative splicing analysis from FASTQ to differential splicing results for short-read bulk RNA-seq. Aligns with STAR 2-pass cohort-style, performs junction QC (RSeQC, MaxEntScan, SpliceAI), runs rMATS-turbo and leafcutter for concordant differential analysis, optionally MAJIQ V3 for complex events / heterogeneous cohorts, isoform-switching with NMD/ORF/domain consequences (IsoformSwitchAnalyzeR v2 + DRIMSeq+DEXSeq+stageR DTU), and sashimi visualizations. Use when performing comprehensive splicing analysis from raw bulk RNA-seq data; for variant-driven splice prediction see splice-variant-prediction; for rare-disease single-patient outlier detection see outlier-splicing-detection; for full-isoform PacBio/ONT analysis see long-read-splicing.
   17 repo stars
8. ▌
   Bio Clinical Biostatistics Subgroup Analysis · gabrielmoreira bundle

   Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RERI for additive interaction, modern data-adaptive HTE methods (STEPP, SIDES, causal forests, X/R-learners), Bayesian shrinkage (Dixon-Simon, MAP, EXNEX), graphical multiplicity (Bretz-Maurer), and credibility frameworks (Sun BMJ, EMA 2019). Use when analyzing treatment effects across patient subgroups for regulatory submissions or precision-medicine claims.
   17 repo stars
9. ▌
   Bio Clinical Biostatistics Survival Analysis · gabrielmoreira bundle

   Performs time-to-event analysis for clinical trials including Cox proportional hazards regression with PH diagnostics, restricted mean survival time (RMST) under non-PH, competing risks via Fine-Gray vs cause-specific Cox, weighted log-rank and MaxCombo for non-proportional hazards, recurrent events (Andersen-Gill, PWP, WLW), and interval-censored data. Use when analyzing time-to-event endpoints (OS, PFS, DOR, TTR, TTNT) in oncology or other clinical trials.
   17 repo stars
10. ▌
    Bio Phylo Tree Manipulation · gabrielmoreira bundle

    Modify phylogenetic tree structure using Biopython Bio.Phylo. Use when rooting trees with outgroups, midpoint, or MAD methods, pruning taxa, collapsing clades, ladderizing branches, or extracting subtrees. Includes rooting method decision guidance.
    17 repo stars
11. ▌
    Bio Rna Quantification Tximport Workflow · gabrielmoreira bundle

    Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta. Use when importing transcript counts into R for DESeq2/edgeR.
    17 repo stars
12. ▌
    Bio Virtual Screening · gabrielmoreira bundle

    Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking docking poses, or selecting a docking workflow for a specific scenario.
    17 repo stars
13. ▌
    Conda Env Manager · gabrielmoreira

    Use this skill whenever the user wants to create, activate, list, export, update, clone, remove, or otherwise manage conda environments, or when a deep-learning / model skill requires a clean, isolated conda environment (e.g. 'create conda env for torch 2.3 cuda', 'export current env to yml', 'list all my conda envs', 'update packages in neuroclaw-dl', 'remove old env', 'clone env for reproducibility', 'install pytorch in new env'). Triggers include: 'conda create', 'conda env', 'make new environment', 'export yml', 'activate env', 'conda list envs', 'update conda env', 'clean environment', 'reproduce env', 'conda remove'. This skill is the mandatory gatekeeper for conda operations: it ALWAYS plans first, shows commands + risks + best practices, and waits for explicit user confirmation before executing anything.
    17 repo stars
14. ▌
    Figure Description · gabrielmoreira

    Process user-provided patent figures and generate formal drawing descriptions. Use when user says "附图处理", "figure description", "附图说明", "drawings description", or wants to describe patent figures with reference numerals.
    17 repo stars
15. ▌
    Monitor Experiment · gabrielmoreira

    Monitor running experiments, check progress, collect results. Use when user says "check results", "is it done", "monitor", or wants experiment output.
    17 repo stars
16. ▌
    Paper Illustration · gabrielmoreira

    Generate publication-quality AI illustrations for academic papers using Gemini image generation. Creates architecture diagrams, method illustrations with Claude-supervised iterative refinement loop. Use when user says "生成图表", "画架构图", "AI绘图", "paper illustration", "generate diagram", or needs visual figures for papers.
    17 repo stars
17. ▌
    Webiny Page Settings Extensions · gabrielmoreira

    Extending the Website Builder page settings with custom settings groups and modifiers. Use this skill when the developer wants to add a new tab/group to the page settings drawer (e.g., Publishing, Analytics, Access Control), or modify an existing settings group (e.g., add fields to General or SEO). Covers PageSettingsGroup, PageSettingsGroupModifier, and the doc.extensions data model. For field types, renderers, and layout details, see the webiny-form-model skill.
    17 repo stars
18. ▌
    Panel Data Guide · gabrielmoreira

    Panel data analysis with fixed and random effects models
    17 repo stars
19. ▌
    Obsidian Zotero Guide · gabrielmoreira

    Insert citations and notes from Zotero into Obsidian knowledge bases
    17 repo stars
20. ▌
    Latex Drawing Collection · gabrielmoreira

    LaTeX drawing examples for Bayesian networks, tensors, and diagrams
    17 repo stars
21. ▌
    Godot Gdscript Patterns · gabrielmoreira

    Master Godot 4 GDScript patterns including signals, scenes, state machines, and optimization. Use when building Godot games, implementing game systems, or learning GDScript best practices.
    17 repo stars
22. ▌
    Tooluniverse Immunotherapy Response Prediction · gabrielmoreira

    Predict patient response to immune checkpoint inhibitors (ICIs) using multi-biomarker integration. Given a cancer type, somatic mutations, and optional biomarkers (TMB, PD-L1, MSI status), performs systematic analysis across 11 phases covering TMB classification, neoantigen burden estimation, MSI/MMR assessment, PD-L1 evaluation, immune microenvironment profiling, mutation-based resistance/sensitivity prediction, clinical evidence retrieval, and multi-biomarker score integration. Generates a quantitative ICI Response Score (0-100), response likelihood tier, specific ICI drug recommendations with evidence, resistance risk factors, and a monitoring plan. Use when oncologists ask about immunotherapy eligibility, checkpoint inhibitor selection, or biomarker-guided ICI treatment decisions.
    17 repo stars
23. ▌
    Tooluniverse Precision Medicine Stratification · gabrielmoreira

    Comprehensive patient stratification for precision medicine by integrating genomic, clinical, and therapeutic data. Given a disease/condition, genomic data (germline variants, somatic mutations, expression), and optional clinical parameters, performs multi-phase analysis across 9 phases covering disease disambiguation, genetic risk assessment, disease-specific molecular stratification, pharmacogenomic profiling, comorbidity/DDI risk, pathway analysis, clinical evidence and guideline mapping, clinical trial matching, and integrated outcome prediction. Generates a quantitative Precision Medicine Risk Score (0-100) with risk tier assignment (Low/Intermediate/High/Very High), treatment algorithm (1st/2nd/3rd line), pharmacogenomic guidance, clinical trial matches, and monitoring plan. Use when clinicians ask about patient risk stratification, treatment selection, prognosis prediction, or personalized therapeutic strategy across cancer, metabolic, cardiovascular, neurological, or rare diseases.
    17 repo stars
24. ▌
    Research Workflows · gabrielmoreira

    Manage project-centric research workflows, claims, evidence, notes, and experiments. Use when the task should be persisted into ResearchClaw's structured research graph instead of remaining a transient chat reply.
    17 repo stars
25. ▌
    Audience Segment Builder · gabrielmoreira

    Use when the user asks to "build audience segments from my customer list", "make value-based / lookalike seed lists", "set up exclusion / suppression segments", or "map audiences to funnel stages across platforms"; turns the user's OWN customer/CRM/GA4 export into seed audiences, value-based lookalike SEED lists, exclusion/suppression segments, and a cross-platform funnel-stage targeting map, informing the ROAS A (Audience) dimension. Not for building account structure or match types — use campaign-architect; not for organic SERP intent — use keyword-research. 付费广告受众分群/种子人群/排除人群/相似人群种子
    17 repo stars
26. ▌
    Outreach Manager · gabrielmoreira

    Use when the user asks to "write influencer outreach", "follow up with a creator", "pitch a journalist, hunter, or launch partner", or "negotiate partnership terms"; produces personalized pitches, multi-touch follow-up sequences, negotiation scripts with objection handling, and a status pipeline tracker — the shared outreach mechanics engine for creator, media/analyst, launch-partner, and social-selling / advocate-recruitment targets. Not for finalizing signed agreements — use contract-helper; not for media-list tiering, embargo terms, or press-release structure — use press-media-relations. 达人邀约建联/合作谈判话术
    17 repo stars
27. ▌
    Competitor Tracker · gabrielmoreira

    Use when the user asks to "track competitor influencer marketing", "see who my rivals partner with", or "benchmark my influencer program"; produces a competitor partnership roster, campaign and content-strategy breakdown, performance estimates, and a gap/opportunity list. Not for finding your own new creators — use influencer-discovery. 竞品达人合作追踪/竞品营销分析
    17 repo stars
28. ▌
    Launch Day Conductor · gabrielmoreira

    Use when the user asks to "run my launch day", "build a launch day runbook / war room", or "decide CONTINUE or ROLLBACK after the push"; produces a pre-conditions gate check (launch-readiness-auditor SHIP verdict + the authoritative date in launch-registry — missing either stops the skill), a dated hour-blocked runbook with owners (morning irreversible pushes, daytime monitoring loop, evening consolidation), a forced observation-window verdict after every irreversible action against pre-declared kill criteria, a P0-P3 incident ladder with rollback playbooks, and T-0 status lines for the registry proposal protocol. Not for channel submission content and platform rules — use community-launch-runner; not for media replies — use press-media-relations. 发布日runbook/作战室/观察窗/回滚裁决/发布日指挥
    17 repo stars
29. ▌
    Performance Monitor · gabrielmoreira

    Use when the user asks to "generate an SEO report", "出月报", "set SEO alerts", or "排名掉了提醒我"; two modes — report builds multi-metric traffic/ranking/authority/content dashboards, and alert configures threshold notifications for future ranking, traffic, technical, backlink, competitor, and AI-visibility changes. Not for raw position-by-position deltas — use rank-tracker. SEO报告/绩效仪表盘/SEO预警/排名监控
    17 repo stars
30. ▌
    Social Calendar Builder · gabrielmoreira

    Use when the user asks to "build our social posting calendar", "set weekly slots and queue depth per channel", or "plan the evergreen recycle rotation"; produces the always-on brand calendar — pillar allocation with hero/hub/help balance and give:ask targets (all labeled Estimated starting heuristics to calibrate against own analytics, never scored rules), per-channel recurring slots with queue depth, a batching workflow, an evergreen recycle cycle with freshness re-checks, deliberate open slots for realtime/trend moments fed by trend-spotter go/skip verdicts, and first-comment/publish-order ops — cadence commitments filed to the channel registry, and no batch ships to the queue without a SHIP verdict from social-quality-auditor pre-publish mode. Not for repurposing an existing asset or the paid-amplification calendar — use content-amplifier. 社媒排期/内容日历/栏目配比/常青循环复用
    17 repo stars
31. ▌
    Social Creative Builder · gabrielmoreira

    Use when the user asks to "turn this idea into posts for every platform", "write the X thread / LinkedIn post / 小红书 note", or "spec the carousel slides"; turns one idea into N platform-native ready-to-paste packages — post/thread, caption, Threads text, 小红书 note, link post with first-comment placement — each adapted per the dated platform norm card (never verbatim cross-posting), every product claim held to approved claims-ledger wording or flagged [needs source], every variant tagged {formula | hook family | CTA type | signal optimized}, plus a carousel slide-spec mode (intro/content/outro slide roles, per-element char budgets, 小红书 3:4 / IG 4:5 / LinkedIn document PDF artboards, text-safe-zone + alt-text checklist). Not for creator deliverable briefs — use brief-generator; not for repurposing existing assets with paid boost — use content-amplifier. 社媒文案/一稿多发改写/小红书笔记/轮播图脚本
    17 repo stars
32. ▌
    Voice Dossier Builder · gabrielmoreira

    Use when the user asks to "codify how our founder sounds", "build a founder voice dossier", or "set our content pillars"; runs an 80%-extraction interview over the user's OWN posts, emails, and decks (never competitor scraping, never an invented persona) and produces the versioned voice record — a per-platform register map (incl. 小红书/微信公众号), banned phrases, per-context disclosure lines (the ECHO C2 upstream), a few-shot bank built exclusively from own posts, and 3-5 content pillars with Estimated %-allocations — submitted via memory/events/channels.ndjson for channel-registry to store as voice-dossier.md, the record every Craft-phase skill reads first. Not for the brand-level voice canon — use brand-language-codifier; not for audience/persona research — use audience-mapper. 声音档案/品牌语气/创始人语气/内容支柱/披露声明
    17 repo stars
33. ▌
    Engagement Inbox Manager · gabrielmoreira

    Use when the user asks to "triage our comments, DMs, and mentions", "draft replies to this thread", "can we repost this fan post", or "set up inbox SLAs and an escalation path"; produces a ranked triage queue with register detection (sincere / ironic / performative / parasocial, sentiment-inversion table included — "this is so bad" under a comedy register is praise), a commenter taxonomy (troll monitor-only / rager / misguided / unhappy-customer / advocate) with a response-tier ladder and per-channel SLAs, an escalation matrix ending at the crisis path, a moderation ladder plus house rules for owned spaces, and a UGC curation-and-rights mode whose dated permission entries route to the channel registry — every reply is a ranked DRAFT a human posts; nothing is ever auto-sent. Not for launch-window feedback triage — use launch-feedback-synthesizer. 评论私信提及分诊/语域识别/回复草稿/UGC授权
    17 repo stars
34. ▌
    Gitnexus Taint Analysis · gabrielmoreira

    Use when working on, reviewing, or extending GitNexus's CFG/taint/PDG subsystem (the `--pdg` layers), or when reasoning about source→sink data-flow findings. Examples: "How does taint analysis work here?", "Why didn't explain find this flow?", "Add a new sink/source", "Review the interprocedural taint code".
    17 repo stars
35. ▌
    Hive Writing Hive Skills · gabrielmoreira

    Author a new Agent Skill for a Hive agent that conforms to the Agent Skills specification (SKILL.md with YAML frontmatter, optional scripts/references/assets directories). Use when the user asks to create, scaffold, add, or package a new skill for a Hive agent.
    17 repo stars
36. ▌
    Yc Advisor · gabrielmoreira bundle

    This skill should be used when the user asks questions about startups, founding decisions, co-founders, fundraising, product development, growth, hiring, or any entrepreneurial advice. It provides access to Y Combinator's complete library of 443 curated resources including essays by Paul Graham, founder interviews, and startup school lectures. Use this skill to give thorough, research-backed advice on startup decisions.
    17 repo stars
37. ▌
    Host Computer Use Linux · gabrielmoreira

    Backend-specific Linux guidance for `computer_use_remote`. Load after `status` or `start_session` reports backend_family `linux`, backend_id `wayland`, or AT-SPI features. Covers AT-SPI structural targeting, Wayland portal caveats, and screenshot verification.
    17 repo stars
38. ▌
    Host Computer Use Macos · gabrielmoreira

    Backend-specific macOS guidance for `computer_use_remote`. Load after `status` or `start_session` reports backend_family/backend_id `macos` or Accessibility-tree features. Covers AX structural targeting, macOS window actions, and screenshot verification.
    17 repo stars
39. ▌
    Terraform CLI Setup · gabrielmoreira

    Terraform CLI 安装与初始化技能。当用户本地未安装 Terraform 时自动完成安装，确保 terraform 命令可用并能执行 init/validate。不负责 Provider 凭证配置，凭证在实际使用时由 terraform-skill 引导。
    17 repo stars
40. ▌
    Input Validation And Sanitization · gabrielmoreira

    Use this skill when implementing any endpoint, form handler, CLI tool, or function that accepts external input. Validate and sanitize all untrusted data before processing — never assume input is safe.
    17 repo stars
41. ▌
    Verify Before Irreversible Action · gabrielmoreira

    Use this skill before taking any action that is hard to reverse — deleting files, overwriting data, sending messages, pushing to remote, modifying production systems. Always pause, state what you are about to do, and confirm before executing.
    17 repo stars
42. ▌
    Bianque · gabrielmoreira

    Evidence-based medical knowledge and research mentor grounded in the Bian Que tradition. Covers clinical reasoning, diagnostic thinking (望闻问切), pharmacology, pathology, differential diagnosis, medical literature appraisal, and the philosophy of early intervention. Trigger whenever users ask about medicine, clinical science, drugs, disease mechanisms, diagnosis, lab interpretation, treatment comparison, or health sciences. Even without explicit research framing, trigger on any topic touching disease, therapeutics, or clinical decision-making. Part of the AIPOCH Medical Research Skill Hub.
    17 repo stars
43. ▌
    Neurokit · gabrielmoreira

    Comprehensive biosignal processing for ECG/PPG/EEG/EDA/RSP/EMG/EOG; use when you need to clean, segment, and extract physiological features for HRV, event-related responses, complexity metrics, or multimodal psychophysiology pipelines.
    17 repo stars
44. ▌
    Buffer Calculator · gabrielmoreira

    Calculate precise buffer recipes with accurate mass and volume measurements for molecular biology and biochemistry. Supports PBS, RIPA, and TAE with concentration scaling, stock solution preparation, pH adjustment guidance, and step-by-step protocols.
    17 repo stars
45. ▌
    Learning Tutoring · gabrielmoreira

    Learning tutoring planning and content production skill for creating study plans, generating exercises, writing answer explanations, and providing review/adjustment guidance; triggered by requests like “study plan”, “exercise set/question bank”, “answer analysis”, “error analysis”, “exam prep plan”, or “spaced/periodic review schedule”.
    17 repo stars
46. ▌
    Meeting Assistant · gabrielmoreira

    Extracts key meeting information in chronological order and outputs decisions and action items; use when you need meeting minutes, action tracking, or project sync notes from transcripts or raw notes.
    17 repo stars
47. ▌
    Slide Deck Images · gabrielmoreira

    Generate professional slide-deck SVG images (not PPTX/PDF) when users ask to “create slides / slide deck / PPT” and need image outputs.
    17 repo stars
48. ▌
    Time Zone Planner · gabrielmoreira

    Plan cross-time-zone meeting windows for distributed teams, providing region-by-region local time mappings and tradeoff analysis for scheduling decisions.
    17 repo stars
49. ▌
    Vector Text Fixer · gabrielmoreira

    Fix garbled text in PDF/SVG vector graphics caused by font encoding issues, making files editable in AI tools. Supports batch processing and JSON export for manual correction.
    17 repo stars
50. ▌
    Ecommerce Video Marketing · gabrielmoreira bundle

    电商运营与内容创作者必备！当您需要为多品类商品策划抖音、小红书等平台的带货视频时，一键生成包含痛点切入、产品展示与专业镜头设计的6阶段高质量视频脚本，轻松打造高转化营销内容，大幅提升品牌销量。
    17 repo stars
51. ▌
    Nanobanana Ppt Visualizer · gabrielmoreira bundle

    平面设计师与内容创作者在制作演示文稿时，当需要将内容大纲转化为高颜值视觉大片，使用此技能可一键生成风格化配图、交互式网页播放器及演示视频，轻松实现从内容规划到视觉呈现的完整闭环，大幅提升汇报演示质感！
    17 repo stars
52. ▌
    Tailored Resume Generator · gabrielmoreira

    软件开发工程师、产品经理等求职者，在针对特定职位描述投递或跨行转岗时，可一键深度分析岗位需求，自动提取ATS关键词并重组个人经验，快速生成高命中率的定制简历，大幅提升面试邀约率。
    17 repo stars
53. ▌
    Hotchocolate Specialist · gabrielmoreira

    Deep HotChocolate v15 GraphQL server expertise — schema design, resolvers, filtering/sorting/projections, pagination, subscriptions, error handling, authorization, performance, persisted operations, source generators, and migration. Self-learns from official docs. Triggers on: HotChocolate, GraphQL filtering/sorting/projections, pagination, subscriptions, mutation conventions, persisted queries, cost analysis, custom scalars, GraphQL authorization, interceptors, source generator, AddTypes, HotChocolate migration, Relay node, UseProjection, UsePaging, UseFiltering, UseSorting.
    17 repo stars
54. ▌
    Testdino Manual Runs · gabrielmoreira

    Use when the user wants to manage a manual execution run or update case-level results inside a run — listing runs, creating runs for a release, inspecting a run, assigning cases, or marking case results (passed/failed/blocked/skipped/retest/untested). Accepts counter-style IDs like RUN-12 and TC-156.
    17 repo stars
55. ▌
    Apple Calendar · gabrielmoreira

    Read macOS Calendar events via the `icalBuddy` CLI and create events via AppleScript (osascript). Use to check the user's calendar, agenda, upcoming events, or add an event on macOS.
    17 repo stars
56. ▌
    Eve Lab Topology Validation · gabrielmoreira

    Validate EVE-NG topology designs and enforce final delivery structure. Use when reviewing a design, checking build readiness, producing the final design output, building an implementation plan, or running topology QA before implementation.
    17 repo stars
57. ▌
    Dataset Transformation · gabrielmoreira

    Generates code that transforms datasets between ML schemas for model training or evaluation. Use when the user says "transform", "convert", "reformat", "change the format", or when a dataset's schema needs to change to match the target format — always use this skill for format changes rather than writing inline transformation code. Supports OpenAI chat, SageMaker SFT/DPO/RLVR/RLAIF, HuggingFace preference, Bedrock Nova, VERL, and custom JSONL formats from local files or S3.
    17 repo stars
58. ▌
    Hyperpod Node Debugger · gabrielmoreira

    Diagnose and remediate per-node issues on a HyperPod cluster (EKS or Slurm) — a specific node is unhealthy, unresponsive, stuck, or needs replacing. Covers on-node EFA, GPU / accelerator hardware (XID, ECC, NVLink, row-remap, DCGM), Slurm node down/drained, disk and memory pressure, per-node lifecycle-script failures, SSM agent, container runtime, kernel panics, pod networking. Read-only. Not for cluster-wide provisioning (→ hyperpod-cluster-debugger), NCCL (→ hyperpod-nccl), or MFU (→ hyperpod-mfu-debugger).
    17 repo stars
59. ▌
    Use Case Specification · gabrielmoreira

    Creates a reusable use case specification file that defines the business problem, stakeholders, and measurable success criteria for model customization, as recommended by the AWS Responsible AI Lens. Use as the default first step in any model customization plan. Skip only if the user explicitly declines or already has a use case specification to reuse. Captures problem statement, primary users, and LLM-as-a-Judge success tenets.
    17 repo stars
60. ▌
    Audit Logging · gabrielmoreira

    Implement centralized audit logging and SIEM integration. Configure log retention and security monitoring. Use when implementing audit trail requirements.
    17 repo stars
61. ▌
    RAG Observability Evals · gabrielmoreira

    Monitor and evaluate RAG systems with retrieval quality metrics, groundedness checks, hallucination detection, and continuous regression testing.
    17 repo stars
62. ▌
    AI Security Hardening · gabrielmoreira

    Harden AI/LLM deployments against prompt injection, data exfiltration, model theft, and supply chain attacks. Covers input validation, output filtering, access control, model API security, and compliance controls for production AI systems.
    17 repo stars
63. ▌
    Unity Project Scout · gabrielmoreira

    Advise on reconnoitering an existing Unity project
    17 repo stars
64. ▌
    Bio Clinical Biostatistics Adaptive Designs · gabrielmoreira bundle

    Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded Cui-Hung-Wang, Mehta-Pocock promising zone), seamless Phase 2/3 with treatment-arm selection, population enrichment, and response-adaptive randomisation. Covers FDA 2019 Final Adaptive Designs Guidance, FDA 2022 Master Protocols, and ICH E20 Step 2b/3 draft (June 2025, NOT final). Use when planning interim analyses, sample-size re-estimation, or master/platform-trial designs.
    17 repo stars
65. ▌
    Bio Admet Prediction · gabrielmoreira bundle

    Predicts ADMET properties using ADMETlab 3.0 (119 endpoints with uncertainty), ADMET-AI, DeepChem MolNet, and chemprop D-MPNN with explicit handling of OECD QSAR principles, applicability domain assessment, calibration, hERG/CYP/AMES gold-standard endpoints, and PAINS / Lipinski / Ro5 / Veber / BBB druglikeness filters. Use when filtering compounds for drug-likeness, prioritizing leads by predicted safety, or building an in-house ADMET QSAR model.
    17 repo stars
66. ▌
    Bio Workflows Atacseq Pipeline · gabrielmoreira bundle

    End-to-end ATAC-seq workflow from FASTQ files to differential accessibility and TF footprinting. Covers alignment, peak calling with MACS3, QC metrics, and optional TOBIAS footprinting. Use when running end-to-end ATAC-seq analysis from FASTQ to differential accessibility.
    17 repo stars
67. ▌
    Bio Crispr Screens Batch Correction · gabrielmoreira bundle

    Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative of including batch as a covariate in MAGeCK MLE or Chronos. Covers screen-specific batch sources (passage cohort, library lot, infection day, sequencing run, Cas9 lot, FBS lot), PCA + variance-decomposition diagnostic to decide if correction is needed, when correction harms biology by over-correcting condition into batch, limma removeBatchEffect for visualization-only correction, and relationship to multi-condition design matrices. Use when combining screens for joint analysis, when passage cohort confounds biology, when DepMap-style panels need Chronos with batch covariates, when picking ComBat vs RUV, or when correction harms biology and should be replaced with explicit covariate modeling.
    17 repo stars
68. ▌
    Bio Batch Processing · gabrielmoreira bundle

    Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.
    17 repo stars
69. ▌
    Bio Workflows Chipseq Pipeline · gabrielmoreira bundle

    End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3 (or HOMER), and peak annotation with ChIPseeker. Use when processing ChIP-seq data from alignment through peak annotation.
    17 repo stars
70. ▌
    Bio Atac Seq Co Accessibility · gabrielmoreira bundle

    Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+. Use when linking enhancer accessibility to promoter accessibility, identifying enhancer-gene pairs from chromatin alone (without paired RNA), running gene-regulatory inference combining ATAC + RNA, or comparing predicted regulatory contacts against Hi-C/Micro-C ground truth.
    17 repo stars
71. ▌
    Bio Compressed Files · gabrielmoreira bundle

    Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with .gz or .bz2 sequence files. Use BGZF for indexable compressed files.
    17 repo stars
72. ▌
    Bio De Visualization · gabrielmoreira bundle

    Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts, plotBCV, sample distance heatmaps, and p-value histograms. Use when visualizing differential expression results.
    17 repo stars
73. ▌
    Bio Restriction Enzyme Selection · gabrielmoreira bundle

    Select restriction enzymes by criteria using Biopython Bio.Restriction. Find enzymes that cut once, don't cut, produce specific overhangs, are commercially available, or have compatible ends for cloning. Use when selecting restriction enzymes for cloning or analysis.
    17 repo stars
74. ▌
    Bio Epitranscriptomics M6a Differential · gabrielmoreira bundle

    Identify differential m6A methylation between conditions from MeRIP-seq. Use when comparing epitranscriptomic changes between treatment groups or cell states.
    17 repo stars
75. ▌
    Bio Epitranscriptomics M6a Peak Calling · gabrielmoreira bundle

    Call m6A peaks from MeRIP-seq IP vs input comparisons. Use when identifying m6A modification sites from methylated RNA immunoprecipitation data.
    17 repo stars
76. ▌
    Bio Longread Medaka · gabrielmoreira bundle

    Polish assemblies and call variants from Oxford Nanopore data using medaka. Uses neural networks trained on specific basecaller versions. Use when improving ONT-only assemblies or calling variants from Nanopore data without short-read polishing.
    17 repo stars
77. ▌
    Bio Experimental Design Multiple Testing · gabrielmoreira bundle

    Applies multiple testing correction methods including FDR, Bonferroni, and q-value for genomics data. Use when filtering differential expression results, setting significance thresholds, or choosing between correction methods for different study designs.
    17 repo stars
78. ▌
    Bio Paired End Fastq · gabrielmoreira bundle

    Handle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data.
    17 repo stars
79. ▌
    Bio Clinical Databases Pharmacogenomics · gabrielmoreira bundle

    Queries PharmGKB / CPIC / DPWG for drug-gene interactions; calls CYP2D6/CYP2C9/CYP2C19/DPYD/TPMT/NUDT15/UGT1A1/SLCO1B1 star alleles and phenotype with PharmCAT, Cyrius (CYP2D6 structural variants), Aldy, Stargazer; applies Caudle 2020 activity-score translation. Use when implementing pharmacogenomic-guided prescribing, applying CPIC vs DPWG guidance, screening HLA risk alleles for ICI / antiepileptics / abacavir, or interpreting compound TPMT+NUDT15 thiopurine risk.
    17 repo stars
80. ▌
    Bio Protac Degraders · gabrielmoreira bundle

    Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (length, composition, rigidity), ternary complex prediction (PRosettaC, DeepTernary, AlphaFold3 with constraints), cooperativity (alpha), DC50 / Dmax characterization, hook effect, and prediction-experiment reconciliation. Use when designing targeted protein degraders, planning linker SAR, predicting ternary complex stability, or building generative degrader workflows.
    17 repo stars
81. ▌
    Bio Phasing Imputation Reference Panels · gabrielmoreira bundle

    Download, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels. Use when setting up imputation infrastructure or selecting appropriate reference panels for target populations.
    17 repo stars
82. ▌
    Bio Workflows Riboseq Pipeline · gabrielmoreira bundle

    End-to-end Ribo-seq analysis from FASTQ to translation efficiency and ORF detection. Use when analyzing ribosome profiling data to study translation.
    17 repo stars
83. ▌
    Bio Sequence Slicing · gabrielmoreira bundle

    Slice, extract, and concatenate biological sequences using Biopython. Use when extracting subsequences, joining sequences, or manipulating sequence regions by position.
    17 repo stars
84. ▌
    Bio Shape Similarity · gabrielmoreira bundle

    Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (electrostatic), and ShaEP with explicit handling of Tanimoto-Combo (shape + color), shape vs ECFP4 complementarity, conformer-ensemble searching, alignment optimization, and scaffold hopping. Use when searching for shape-mimicking compounds with different scaffolds, identifying bioisosteric replacements, prospective scaffold hopping, or expanding hit series beyond 2D similarity.
    17 repo stars
85. ▌
    Bio Atac Seq Single Cell Atac · gabrielmoreira bundle

    Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X scATAC or 10X Multiome (paired RNA+ATAC) data, performing per-cell QC, choosing between ArchR/Signac/SnapATAC2 ecosystems, building per-cluster consensus peaksets, integrating with paired scRNA-seq, doublet detection (AMULET vs ArchR vs scDblFinder), or running pseudobulk differential accessibility per cluster.
    17 repo stars
86. ▌
    Bio Comparative Genomics Synteny Analysis · gabrielmoreira bundle

    Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.
    17 repo stars
87. ▌
    Bio Vcf Manipulation · gabrielmoreira bundle

    Merge, concatenate, sort, intersect, and subset VCF files using bcftools. Use when combining variant files, comparing call sets, or restructuring VCF data.
    17 repo stars
88. ▌
    Proteinmpnn · gabrielmoreira

    Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. 2022, github.com/dauparas/ProteinMPNN). Reach for this skill to run sequence design on RFdiffusion backbones, to redesign one chain of a PDB while holding interface residues fixed, or to generate a temperature-swept set of sequences for downstream folding.
    17 repo stars
89. ▌
    Solublempnn · gabrielmoreira

    Inverse-fold a backbone with SolubleMPNN — ProteinMPNN retrained on a soluble-PDB subset (Dauparas et al. 2022) — for sequences biased toward cytosolic expression and reduced aggregation. Reach for this skill when designs from vanilla ProteinMPNN are aggregating or going to inclusion bodies, when redesigning a membrane-adjacent fold for soluble expression, or when an E. coli expression screen is the next step.
    17 repo stars
90. ▌
    Druglib Reviews · gabrielmoreira bundle

    Query the DrugLib.com Drug Review Dataset (UCI #461). Use whenever the user asks about patient drug reviews, drug effectiveness ratings, side-effect profiles, or condition-specific treatment experiences from DrugLib.com.
    17 repo stars
91. ▌
    Molecular Targets Query · gabrielmoreira bundle

    Query the NCI CCDI Molecular Targets Platform (pediatric oncology) for targets (genes), diseases, drugs, and target-disease associations via its public GraphQL API. Auto-detects entity type from input string.
    17 repo stars
92. ▌
    Experiment Craft · gabrielmoreira

    Use this skill when the user wants to debug, diagnose, or systematically iterate on an experiment that already exists, or when they need a structured experiment log for tracking runs, hypotheses, failures, results, and next steps during active research. Apply it to underperforming methods, training that will not converge, regressions after a change, inconsistent results across datasets, aimless experimentation without progress, and questions like 'why doesn't this work?', 'no progress after many attempts', or 'how should I investigate this failure?'. Also use it for setting up practical experiment logging/record-keeping that supports debugging and iteration. Do not use it for designing a brand-new experiment pipeline or full experiment program (use experiment-pipeline), generating research ideas, fixing isolated coding/syntax errors, or writing retrospective summaries into research memory/notes/knowledge bases.
    17 repo stars
93. ▌
    Hcppipeline Tool · gabrielmoreira

    Use this skill whenever the user wants to perform high-quality, HCP-style preprocessing of multimodal MRI data (structural, functional, diffusion) using the official HCP Pipelines. Triggers include: 'HCP pipeline', 'HCP preprocessing', 'hcp-fmri', 'hcp-dwi', 'hcp-structural', 'MSMAll', 'ICA-FIX', 'bedpostx', 'probtrackx', or any request to run the Human Connectome Project preprocessing pipelines.
    17 repo stars
94. ▌
    Wmh Segmentation · gabrielmoreira

    Use this skill whenever the user wants to perform automated white matter hyperintensity (WMH) segmentation on structural MRI data using the MARS-WMH nnU-Net model. Requires one FLAIR and one T1w NIfTI image (no contrast). Triggers include: 'wmh', 'white matter hyperintensities', 'WMH segmentation', 'MARS-WMH', 'wmh-nnunet', 'segment FLAIR T1', 'white matter lesions', 'vascular WMH', 'mars wmh', or any request to run nnU-Net WMH segmentation on FLAIR+T1w pair.
    17 repo stars
95. ▌
    Bio Reads Qc Mapping · gabrielmoreira bundle

    Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.
    17 repo stars
96. ▌
    Sc Best Practices Skills Index · gabrielmoreira bundle

    Skills derived from the Single-cell Best Practices book (sc-best-practices.org). Comprehensive workflows and guidelines for single-cell and spatial omics analysis.
    17 repo stars
97. ▌
    Cell Figure Guide · gabrielmoreira

    Cell (Cell Press) figure preparation: resolution (300-1000 DPI), formats (TIFF/PDF), RGB color, Avenir/Arial fonts, uppercase panel labels, strict image manipulation policies.
    17 repo stars
98. ▌
    Interpro Database · gabrielmoreira

    Query InterPro REST API for protein domain architecture, family classification, and member-DB integration. Search entries, retrieve a protein's domains, list family members, get taxonomic distribution, link to PDB. Unifies Pfam, PANTHER, PIRSF, PRINTS, PROSITE, SMART, CDD, NCBIfam. Use uniprot-protein-database for sequences; pdb-database for 3D structures.
    17 repo stars
99. ▌
    Reactome Database · gabrielmoreira

    Query Reactome pathways via REST: pathway queries, entity lookup, keyword search, gene list enrichment, hierarchy, cross-refs. Content + Analysis services. Python wrapper: reactome2py. For KEGG use kegg-database; for PPIs use string-database-ppi.
    17 repo stars
100. ▌
     Developer Utilities Get Base64 · gabrielmoreira

     Generate a QR code for any string and return a base64-encoded PNG. Configurable size and error correction level.
     17 repo stars